Index: modules/user.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/user.module,v
retrieving revision 1.578
diff -u -p -r1.578 user.module
--- modules/user.module	2 Feb 2006 01:51:54 -0000	1.578
+++ modules/user.module	8 Feb 2006 18:34:09 -0000
@@ -1624,20 +1625,36 @@ function user_admin_perm($str_rids = NUL
       $form['permission'][] = array('#type' => 'markup', '#value' => t('%module module', array('%module' => $module)));
       asort($permissions);
       foreach ($permissions as $perm) {
+        $row_visible = FALSE;
         $options[$perm] = '';
-        $form['permission'][$perm] = array('#type' => 'markup', '#value' => t($perm));
         foreach ($role_names as $rid => $name) {
           // Builds arrays for checked boxes for each role
           if (strstr($role_permissions[$rid], $perm)) {
-            $status[$rid][] = $perm;
+            if (user_access($perm)) {
+              $status[$rid][] = $perm;
+              $row_visible = TRUE;
+            }
+            else {
+              // submit would delete the permission without this
+              $form_fixed['checkboxes'][$rid][$perm] = array('#type' => 'value', '#value' => 1);
+            }
+          }
+          else {
+            // an empty markup form element
+            $form_fixed['checkboxes'][$rid][$perm] = array();
           }
         }
+        if ($row_visible) {
+          $form['permission'][$perm] = array('#type' => 'markup', '#value' => t($perm));
+        }
       }
     }
   }
+
   // Have to build checkboxes here after checkbox arrays are built
   foreach ($role_names as $rid => $name) {
     $form['checkboxes'][$rid] = array('#type' => 'checkboxes', '#options' => $options, '#default_value' => $status[$rid]);
+    $form['checkboxes'][$rid] = array_merge($form['checkboxes'][$rid], (array)$form_fixed['checkboxes'][$rid]);
     $form['role_names'][$rid] = array('#type' => 'markup', '#value' => l($name, 'admin/access/'. $rid), '#tree' => TRUE);
   }
   $form['submit'] = array('#type' => 'submit', '#value' => t('Save permissions'));